A substrate processing apparatus provided with an ion beam generator is available as a technology for performing high-precision and uniform microfabrication and planarization processing of a surface for microfabrication of a semiconductor substrate and a magnetic disk substrate. Published Japanese Patent Application No. JP-A S60-127732 discloses a semiconductor processing apparatus that has an accelerating grid disposed obliquely relative to the surface of a semiconductor in order to perform high-precision surface processing. And, Published Japanese Patent Application No. JP-A 2008-117753 discloses an ion gun in which a lead-out electrode portion is disposed obliquely at both sides of a reference plane, and both sides of a substrate are planarized simultaneously.